3EWZ

human orotidyl-5'-monophosphate decarboxylase in complex with 5-cyano-UMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP83000.1 M Tris-HCl pH 8.0, 1.8 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K
Crystal Properties
Matthews coefficientSolvent content
2.5852.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.557α = 90
b = 60.793β = 99.29
c = 136.087γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.446.0885.30.0699.62.6193472
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4635.60.3781.50.78026

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.446.08177695935582.480.155930.15430.18701RANDOM10.678
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.42-0.76-0.380.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.327
r_dihedral_angle_4_deg15.341
r_dihedral_angle_3_deg12.988
r_dihedral_angle_1_deg5.992
r_sphericity_free4.384
r_scangle_it3.753
r_angle_other_deg2.721
r_scbond_it2.42
r_sphericity_bonded1.851
r_mcangle_it1.589
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.327
r_dihedral_angle_4_deg15.341
r_dihedral_angle_3_deg12.988
r_dihedral_angle_1_deg5.992
r_sphericity_free4.384
r_scangle_it3.753
r_angle_other_deg2.721
r_scbond_it2.42
r_sphericity_bonded1.851
r_mcangle_it1.589
r_angle_refined_deg1.487
r_rigid_bond_restr1.136
r_mcbond_it0.974
r_mcbond_other0.382
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8275
Nucleic Acid Atoms
Solvent Atoms1248
Heterogen Atoms102

Software

Software
Software NamePurpose
COMOphasing
REFMACrefinement
XDSdata reduction
SADABSdata scaling